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39 * \brief This file defines functions used by the domdec module
40 * while managing the construction, use and error checking for
41 * topologies local to a DD rank.
43 * \author Berk Hess <hess@kth.se>
44 * \ingroup module_domdec
57 #include "gromacs/domdec/domdec.h"
58 #include "gromacs/domdec/domdec_network.h"
59 #include "gromacs/domdec/ga2la.h"
60 #include "gromacs/gmxlib/chargegroup.h"
61 #include "gromacs/gmxlib/network.h"
62 #include "gromacs/math/vec.h"
63 #include "gromacs/mdlib/forcerec.h"
64 #include "gromacs/mdlib/gmx_omp_nthreads.h"
65 #include "gromacs/mdtypes/commrec.h"
66 #include "gromacs/mdtypes/inputrec.h"
67 #include "gromacs/mdtypes/md_enums.h"
68 #include "gromacs/mdtypes/mdatom.h"
69 #include "gromacs/mdtypes/state.h"
70 #include "gromacs/pbcutil/mshift.h"
71 #include "gromacs/pbcutil/pbc.h"
72 #include "gromacs/topology/ifunc.h"
73 #include "gromacs/topology/mtop_util.h"
74 #include "gromacs/topology/topsort.h"
75 #include "gromacs/utility/cstringutil.h"
76 #include "gromacs/utility/exceptions.h"
77 #include "gromacs/utility/fatalerror.h"
78 #include "gromacs/utility/gmxassert.h"
79 #include "gromacs/utility/logger.h"
80 #include "gromacs/utility/smalloc.h"
81 #include "gromacs/utility/strconvert.h"
82 #include "gromacs/utility/stringstream.h"
83 #include "gromacs/utility/stringutil.h"
84 #include "gromacs/utility/textwriter.h"
86 #include "domdec_constraints.h"
87 #include "domdec_internal.h"
88 #include "domdec_vsite.h"
91 /*! \brief The number of integer item in the local state, used for broadcasting of the state */
92 #define NITEM_DD_INIT_LOCAL_STATE 5
94 struct reverse_ilist_t
96 std::vector<int> index; /* Index for each atom into il */
97 std::vector<int> il; /* ftype|type|a0|...|an|ftype|... */
98 int numAtomsInMolecule; /* The number of atoms in this molecule */
101 struct MolblockIndices
109 /*! \brief Struct for thread local work data for local topology generation */
112 t_idef idef; /**< Partial local topology */
113 std::unique_ptr<VsitePbc> vsitePbc; /**< vsite PBC structure */
114 int nbonded; /**< The number of bondeds in this struct */
115 t_blocka excl; /**< List of exclusions */
116 int excl_count; /**< The total exclusion count for \p excl */
119 /*! \brief Struct for the reverse topology: links bonded interactions to atomsx */
120 struct gmx_reverse_top_t
122 //! @cond Doxygen_Suppress
123 //! \brief Do we require all exclusions to be assigned?
124 bool bExclRequired = false;
125 //! \brief The maximum number of exclusions one atom can have
126 int n_excl_at_max = 0;
127 //! \brief Are there constraints in this revserse top?
128 bool bConstr = false;
129 //! \brief Are there settles in this revserse top?
130 bool bSettle = false;
131 //! \brief All bonded interactions have to be assigned?
132 bool bBCheck = false;
133 //! \brief Are there bondeds/exclusions between charge-groups?
134 bool bInterCGInteractions = false;
135 //! \brief Reverse ilist for all moltypes
136 std::vector<reverse_ilist_t> ril_mt;
137 //! \brief The size of ril_mt[?].index summed over all entries
138 int ril_mt_tot_size = 0;
139 //! \brief The sorting state of bondeds for free energy
140 int ilsort = ilsortUNKNOWN;
141 //! \brief molblock to global atom index for quick lookup of molblocks on atom index
142 std::vector<MolblockIndices> mbi;
144 //! \brief Do we have intermolecular interactions?
145 bool bIntermolecularInteractions = false;
146 //! \brief Intermolecular reverse ilist
147 reverse_ilist_t ril_intermol;
149 /* Work data structures for multi-threading */
150 //! \brief Thread work array for local topology generation
151 std::vector<thread_work_t> th_work;
155 /*! \brief Returns the number of atom entries for il in gmx_reverse_top_t */
156 static int nral_rt(int ftype)
161 if (interaction_function[ftype].flags & IF_VSITE)
163 /* With vsites the reverse topology contains an extra entry
164 * for storing if constructing atoms are vsites.
172 /*! \brief Return whether interactions of type \p ftype need to be assigned exactly once */
173 static gmx_bool dd_check_ftype(int ftype, gmx_bool bBCheck,
174 gmx_bool bConstr, gmx_bool bSettle)
176 return ((((interaction_function[ftype].flags & IF_BOND) != 0u) &&
177 ((interaction_function[ftype].flags & IF_VSITE) == 0u) &&
178 (bBCheck || ((interaction_function[ftype].flags & IF_LIMZERO) == 0u))) ||
179 (bConstr && (ftype == F_CONSTR || ftype == F_CONSTRNC)) ||
180 (bSettle && ftype == F_SETTLE));
183 /*! \brief Help print error output when interactions are missing */
185 print_missing_interactions_mb(t_commrec *cr,
186 const gmx_reverse_top_t *rt,
187 const char *moltypename,
188 const reverse_ilist_t *ril,
189 int a_start, int a_end,
190 int nat_mol, int nmol,
194 int nril_mol = ril->index[nat_mol];
195 snew(assigned, nmol*nril_mol);
196 gmx::StringOutputStream stream;
197 gmx::TextWriter log(&stream);
199 gmx::ArrayRef<const int> gatindex = cr->dd->globalAtomIndices;
200 for (int ftype = 0; ftype < F_NRE; ftype++)
202 if (dd_check_ftype(ftype, rt->bBCheck, rt->bConstr, rt->bSettle))
204 int nral = NRAL(ftype);
205 const t_ilist *il = &idef->il[ftype];
206 const t_iatom *ia = il->iatoms;
207 for (int i = 0; i < il->nr; i += 1+nral)
209 int a0 = gatindex[ia[1]];
210 /* Check if this interaction is in
211 * the currently checked molblock.
213 if (a0 >= a_start && a0 < a_end)
215 int mol = (a0 - a_start)/nat_mol;
216 int a0_mol = (a0 - a_start) - mol*nat_mol;
217 int j_mol = ril->index[a0_mol];
219 while (j_mol < ril->index[a0_mol+1] && !found)
221 int j = mol*nril_mol + j_mol;
222 int ftype_j = ril->il[j_mol];
223 /* Here we need to check if this interaction has
224 * not already been assigned, since we could have
225 * multiply defined interactions.
227 if (ftype == ftype_j && ia[0] == ril->il[j_mol+1] &&
230 /* Check the atoms */
232 for (int a = 0; a < nral; a++)
234 if (gatindex[ia[1+a]] !=
235 a_start + mol*nat_mol + ril->il[j_mol+2+a])
245 j_mol += 2 + nral_rt(ftype_j);
249 gmx_incons("Some interactions seem to be assigned multiple times");
257 gmx_sumi(nmol*nril_mol, assigned, cr);
261 for (int mol = 0; mol < nmol; mol++)
264 while (j_mol < nril_mol)
266 int ftype = ril->il[j_mol];
267 int nral = NRAL(ftype);
268 int j = mol*nril_mol + j_mol;
269 if (assigned[j] == 0 &&
270 !(interaction_function[ftype].flags & IF_VSITE))
272 if (DDMASTER(cr->dd))
276 log.writeLineFormatted("Molecule type '%s'", moltypename);
277 log.writeLineFormatted(
278 "the first %d missing interactions, except for exclusions:", nprint);
280 log.writeStringFormatted("%20s atoms",
281 interaction_function[ftype].longname);
283 for (a = 0; a < nral; a++)
285 log.writeStringFormatted("%5d", ril->il[j_mol+2+a]+1);
289 log.writeString(" ");
292 log.writeString(" global");
293 for (a = 0; a < nral; a++)
295 log.writeStringFormatted("%6d",
296 a_start+mol*nat_mol+ril->il[j_mol+2+a]+1);
298 log.ensureLineBreak();
306 j_mol += 2 + nral_rt(ftype);
311 return stream.toString();
314 /*! \brief Help print error output when interactions are missing */
315 static void print_missing_interactions_atoms(const gmx::MDLogger &mdlog,
317 const gmx_mtop_t *mtop,
320 const gmx_reverse_top_t *rt = cr->dd->reverse_top;
322 /* Print the atoms in the missing interactions per molblock */
324 for (const gmx_molblock_t &molb : mtop->molblock)
326 const gmx_moltype_t &moltype = mtop->moltype[molb.type];
328 a_end = a_start + molb.nmol*moltype.atoms.nr;
330 GMX_LOG(mdlog.warning).appendText(
331 print_missing_interactions_mb(cr, rt,
333 &rt->ril_mt[molb.type],
334 a_start, a_end, moltype.atoms.nr,
340 void dd_print_missing_interactions(const gmx::MDLogger &mdlog,
343 const gmx_mtop_t *top_global,
344 const gmx_localtop_t *top_local,
345 const t_state *state_local)
347 int ndiff_tot, cl[F_NRE], n, ndiff, rest_global, rest_local;
353 GMX_LOG(mdlog.warning).appendText(
354 "Not all bonded interactions have been properly assigned to the domain decomposition cells");
356 ndiff_tot = local_count - dd->nbonded_global;
358 for (ftype = 0; ftype < F_NRE; ftype++)
361 cl[ftype] = top_local->idef.il[ftype].nr/(1+nral);
364 gmx_sumi(F_NRE, cl, cr);
368 GMX_LOG(mdlog.warning).appendText("A list of missing interactions:");
369 rest_global = dd->nbonded_global;
370 rest_local = local_count;
371 for (ftype = 0; ftype < F_NRE; ftype++)
373 /* In the reverse and local top all constraints are merged
374 * into F_CONSTR. So in the if statement we skip F_CONSTRNC
375 * and add these constraints when doing F_CONSTR.
377 if (((interaction_function[ftype].flags & IF_BOND) &&
378 (dd->reverse_top->bBCheck
379 || !(interaction_function[ftype].flags & IF_LIMZERO)))
380 || (dd->reverse_top->bConstr && ftype == F_CONSTR)
381 || (dd->reverse_top->bSettle && ftype == F_SETTLE))
383 n = gmx_mtop_ftype_count(top_global, ftype);
384 if (ftype == F_CONSTR)
386 n += gmx_mtop_ftype_count(top_global, F_CONSTRNC);
388 ndiff = cl[ftype] - n;
391 GMX_LOG(mdlog.warning).appendTextFormatted(
392 "%20s of %6d missing %6d",
393 interaction_function[ftype].longname, n, -ndiff);
396 rest_local -= cl[ftype];
400 ndiff = rest_local - rest_global;
403 GMX_LOG(mdlog.warning).appendTextFormatted(
404 "%20s of %6d missing %6d", "exclusions",
405 rest_global, -ndiff);
409 print_missing_interactions_atoms(mdlog, cr, top_global, &top_local->idef);
410 write_dd_pdb("dd_dump_err", 0, "dump", top_global, cr,
411 -1, state_local->x.rvec_array(), state_local->box);
413 std::string errorMessage;
417 errorMessage = "One or more interactions were assigned to multiple domains of the domain decompostion. Please report this bug.";
421 errorMessage = gmx::formatString("%d of the %d bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (%g nm) or the two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck", -ndiff_tot, cr->dd->nbonded_global, dd_cutoff_multibody(dd), dd_cutoff_twobody(dd));
423 gmx_fatal_collective(FARGS, cr->mpi_comm_mygroup, MASTER(cr), "%s", errorMessage.c_str());
426 /*! \brief Return global topology molecule information for global atom index \p i_gl */
427 static void global_atomnr_to_moltype_ind(const gmx_reverse_top_t *rt,
429 int *mb, int *mt, int *mol, int *i_mol)
431 const MolblockIndices *mbi = rt->mbi.data();
433 int end = rt->mbi.size(); /* exclusive */
436 /* binary search for molblock_ind */
440 if (i_gl >= mbi[mid].a_end)
444 else if (i_gl < mbi[mid].a_start)
458 *mol = (i_gl - mbi->a_start) / mbi->natoms_mol;
459 *i_mol = (i_gl - mbi->a_start) - (*mol)*mbi->natoms_mol;
462 /*! \brief Count the exclusions for all atoms in \p cgs */
463 static void count_excls(const t_block *cgs, const t_blocka *excls,
464 int *n_excl, int *n_intercg_excl, int *n_excl_at_max)
466 int cg, at0, at1, at, excl, atj;
471 for (cg = 0; cg < cgs->nr; cg++)
473 at0 = cgs->index[cg];
474 at1 = cgs->index[cg+1];
475 for (at = at0; at < at1; at++)
477 for (excl = excls->index[at]; excl < excls->index[at+1]; excl++)
479 atj = excls->a[excl];
483 if (atj < at0 || atj >= at1)
490 *n_excl_at_max = std::max(*n_excl_at_max,
491 excls->index[at+1] - excls->index[at]);
496 /*! \brief Run the reverse ilist generation and store it in r_il when \p bAssign = TRUE */
497 static int low_make_reverse_ilist(const InteractionLists &il_mt,
500 gmx_bool bConstr, gmx_bool bSettle,
502 gmx::ArrayRef<const int> r_index,
503 gmx::ArrayRef<int> r_il,
504 gmx_bool bLinkToAllAtoms,
507 int ftype, j, nlink, link;
512 for (ftype = 0; ftype < F_NRE; ftype++)
514 if ((interaction_function[ftype].flags & (IF_BOND | IF_VSITE)) ||
515 (bConstr && (ftype == F_CONSTR || ftype == F_CONSTRNC)) ||
516 (bSettle && ftype == F_SETTLE))
518 const bool bVSite = ((interaction_function[ftype].flags & IF_VSITE) != 0u);
519 const int nral = NRAL(ftype);
520 const auto &il = il_mt[ftype];
521 for (int i = 0; i < il.size(); i += 1+nral)
523 const int* ia = il.iatoms.data() + i;
528 /* We don't need the virtual sites for the cg-links */
538 /* Couple to the first atom in the interaction */
541 for (link = 0; link < nlink; link++)
546 GMX_ASSERT(!r_il.empty(), "with bAssign not allowed to be empty");
547 GMX_ASSERT(!r_index.empty(), "with bAssign not allowed to be empty");
548 r_il[r_index[a]+count[a]] =
549 (ftype == F_CONSTRNC ? F_CONSTR : ftype);
550 r_il[r_index[a]+count[a]+1] = ia[0];
551 for (j = 1; j < 1+nral; j++)
553 /* Store the molecular atom number */
554 r_il[r_index[a]+count[a]+1+j] = ia[j];
557 if (interaction_function[ftype].flags & IF_VSITE)
561 /* Add an entry to iatoms for storing
562 * which of the constructing atoms are
565 r_il[r_index[a]+count[a]+2+nral] = 0;
566 for (j = 2; j < 1+nral; j++)
568 if (atom[ia[j]].ptype == eptVSite)
570 r_il[r_index[a]+count[a]+2+nral] |= (2<<j);
577 /* We do not count vsites since they are always
578 * uniquely assigned and can be assigned
579 * to multiple nodes with recursive vsites.
582 !(interaction_function[ftype].flags & IF_LIMZERO))
587 count[a] += 2 + nral_rt(ftype);
596 /*! \brief Make the reverse ilist: a list of bonded interactions linked to atoms */
597 static int make_reverse_ilist(const InteractionLists &ilist,
598 const t_atoms *atoms,
599 gmx_bool bConstr, gmx_bool bSettle,
601 gmx_bool bLinkToAllAtoms,
602 reverse_ilist_t *ril_mt)
604 int nat_mt, *count, i, nint_mt;
606 /* Count the interactions */
609 low_make_reverse_ilist(ilist, atoms->atom,
611 bConstr, bSettle, bBCheck,
613 bLinkToAllAtoms, FALSE);
615 ril_mt->index.push_back(0);
616 for (i = 0; i < nat_mt; i++)
618 ril_mt->index.push_back(ril_mt->index[i] + count[i]);
621 ril_mt->il.resize(ril_mt->index[nat_mt]);
623 /* Store the interactions */
625 low_make_reverse_ilist(ilist, atoms->atom,
627 bConstr, bSettle, bBCheck,
628 ril_mt->index, ril_mt->il,
629 bLinkToAllAtoms, TRUE);
633 ril_mt->numAtomsInMolecule = atoms->nr;
638 /*! \brief Generate the reverse topology */
639 static gmx_reverse_top_t make_reverse_top(const gmx_mtop_t *mtop, gmx_bool bFE,
640 gmx_bool bConstr, gmx_bool bSettle,
641 gmx_bool bBCheck, int *nint)
643 gmx_reverse_top_t rt;
645 /* Should we include constraints (for SHAKE) in rt? */
646 rt.bConstr = bConstr;
647 rt.bSettle = bSettle;
648 rt.bBCheck = bBCheck;
650 rt.bInterCGInteractions = mtop->bIntermolecularInteractions;
651 rt.ril_mt.resize(mtop->moltype.size());
652 rt.ril_mt_tot_size = 0;
653 std::vector<int> nint_mt;
654 for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
656 const gmx_moltype_t &molt = mtop->moltype[mt];
659 rt.bInterCGInteractions = true;
662 /* Make the atom to interaction list for this molecule type */
663 int numberOfInteractions =
664 make_reverse_ilist(molt.ilist, &molt.atoms,
665 rt.bConstr, rt.bSettle, rt.bBCheck, FALSE,
667 nint_mt.push_back(numberOfInteractions);
669 rt.ril_mt_tot_size += rt.ril_mt[mt].index[molt.atoms.nr];
673 fprintf(debug, "The total size of the atom to interaction index is %d integers\n", rt.ril_mt_tot_size);
677 for (const gmx_molblock_t &molblock : mtop->molblock)
679 *nint += molblock.nmol*nint_mt[molblock.type];
682 /* Make an intermolecular reverse top, if necessary */
683 rt.bIntermolecularInteractions = mtop->bIntermolecularInteractions;
684 if (rt.bIntermolecularInteractions)
686 t_atoms atoms_global;
688 atoms_global.nr = mtop->natoms;
689 atoms_global.atom = nullptr; /* Only used with virtual sites */
691 GMX_RELEASE_ASSERT(mtop->intermolecular_ilist, "We should have an ilist when intermolecular interactions are on");
694 make_reverse_ilist(*mtop->intermolecular_ilist,
696 rt.bConstr, rt.bSettle, rt.bBCheck, FALSE,
700 if (bFE && gmx_mtop_bondeds_free_energy(mtop))
702 rt.ilsort = ilsortFE_UNSORTED;
706 rt.ilsort = ilsortNO_FE;
709 /* Make a molblock index for fast searching */
711 for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
713 const gmx_molblock_t &molb = mtop->molblock[mb];
714 const int numAtomsPerMol = mtop->moltype[molb.type].atoms.nr;
717 i += molb.nmol*numAtomsPerMol;
719 mbi.natoms_mol = numAtomsPerMol;
720 mbi.type = molb.type;
721 rt.mbi.push_back(mbi);
724 rt.th_work.resize(gmx_omp_nthreads_get(emntDomdec));
729 void dd_make_reverse_top(FILE *fplog,
730 gmx_domdec_t *dd, const gmx_mtop_t *mtop,
731 const gmx_vsite_t *vsite,
732 const t_inputrec *ir, gmx_bool bBCheck)
736 fprintf(fplog, "\nLinking all bonded interactions to atoms\n");
739 /* If normal and/or settle constraints act only within charge groups,
740 * we can store them in the reverse top and simply assign them to domains.
741 * Otherwise we need to assign them to multiple domains and set up
742 * the parallel version constraint algorithm(s).
745 dd->reverse_top = new gmx_reverse_top_t;
747 make_reverse_top(mtop, ir->efep != efepNO,
748 !dd->splitConstraints, !dd->splitSettles,
749 bBCheck, &dd->nbonded_global);
751 gmx_reverse_top_t *rt = dd->reverse_top;
753 /* With the Verlet scheme, exclusions are handled in the non-bonded
754 * kernels and only exclusions inside the cut-off lead to exclusion
755 * forces. Since each atom pair is treated at most once in the non-bonded
756 * kernels, it doesn't matter if the exclusions for the same atom pair
757 * appear multiple times in the exclusion list. In contrast, the, old,
758 * group cut-off scheme loops over a list of exclusions, so there each
759 * excluded pair should appear exactly once.
761 rt->bExclRequired = (ir->cutoff_scheme == ecutsGROUP &&
762 inputrecExclForces(ir));
765 dd->n_intercg_excl = 0;
766 rt->n_excl_at_max = 0;
767 for (const gmx_molblock_t &molb : mtop->molblock)
769 int n_excl_mol, n_excl_icg, n_excl_at_max;
771 const gmx_moltype_t &molt = mtop->moltype[molb.type];
772 count_excls(&molt.cgs, &molt.excls,
773 &n_excl_mol, &n_excl_icg, &n_excl_at_max);
774 nexcl += molb.nmol*n_excl_mol;
775 dd->n_intercg_excl += molb.nmol*n_excl_icg;
776 rt->n_excl_at_max = std::max(rt->n_excl_at_max, n_excl_at_max);
778 if (rt->bExclRequired)
780 dd->nbonded_global += nexcl;
781 if (EEL_FULL(ir->coulombtype) && dd->n_intercg_excl > 0 && fplog)
783 fprintf(fplog, "There are %d inter charge-group exclusions,\n"
784 "will use an extra communication step for exclusion forces for %s\n",
785 dd->n_intercg_excl, eel_names[ir->coulombtype]);
789 if (vsite && vsite->numInterUpdategroupVsites > 0)
793 fprintf(fplog, "There are %d inter update-group virtual sites,\n"
794 "will an extra communication step for selected coordinates and forces\n",
795 vsite->numInterUpdategroupVsites);
797 init_domdec_vsites(dd, vsite->numInterUpdategroupVsites);
800 if (dd->splitConstraints || dd->splitSettles)
802 init_domdec_constraints(dd, mtop);
806 fprintf(fplog, "\n");
810 /*! \brief Store a vsite interaction at the end of \p il
812 * This routine is very similar to add_ifunc, but vsites interactions
813 * have more work to do than other kinds of interactions, and the
814 * complex way nral (and thus vector contents) depends on ftype
815 * confuses static analysis tools unless we fuse the vsite
816 * atom-indexing organization code with the ifunc-adding code, so that
817 * they can see that nral is the same value. */
819 add_ifunc_for_vsites(t_iatom *tiatoms, const gmx_ga2la_t &ga2la,
820 int nral, gmx_bool bHomeA,
821 int a, int a_gl, int a_mol,
822 const t_iatom *iatoms,
827 if (il->nr+1+nral > il->nalloc)
829 il->nalloc = over_alloc_large(il->nr+1+nral);
830 srenew(il->iatoms, il->nalloc);
832 liatoms = il->iatoms + il->nr;
836 tiatoms[0] = iatoms[0];
840 /* We know the local index of the first atom */
845 /* Convert later in make_local_vsites */
846 tiatoms[1] = -a_gl - 1;
849 for (int k = 2; k < 1+nral; k++)
851 int ak_gl = a_gl + iatoms[k] - a_mol;
852 if (const int *homeIndex = ga2la.findHome(ak_gl))
854 tiatoms[k] = *homeIndex;
858 /* Copy the global index, convert later in make_local_vsites */
859 tiatoms[k] = -(ak_gl + 1);
861 // Note that ga2la_get_home always sets the third parameter if
864 for (int k = 0; k < 1+nral; k++)
866 liatoms[k] = tiatoms[k];
870 /*! \brief Store a bonded interaction at the end of \p il */
871 static inline void add_ifunc(int nral, const t_iatom *tiatoms, t_ilist *il)
876 if (il->nr+1+nral > il->nalloc)
878 il->nalloc = over_alloc_large(il->nr+1+nral);
879 srenew(il->iatoms, il->nalloc);
881 liatoms = il->iatoms + il->nr;
882 for (k = 0; k <= nral; k++)
884 liatoms[k] = tiatoms[k];
889 /*! \brief Store a position restraint in idef and iatoms, complex because the parameters are different for each entry */
890 static void add_posres(int mol, int a_mol, int numAtomsInMolecule,
891 const gmx_molblock_t *molb,
892 t_iatom *iatoms, const t_iparams *ip_in,
898 /* This position restraint has not been added yet,
899 * so it's index is the current number of position restraints.
901 n = idef->il[F_POSRES].nr/2;
902 if (n+1 > idef->iparams_posres_nalloc)
904 idef->iparams_posres_nalloc = over_alloc_dd(n+1);
905 srenew(idef->iparams_posres, idef->iparams_posres_nalloc);
907 ip = &idef->iparams_posres[n];
908 /* Copy the force constants */
909 *ip = ip_in[iatoms[0]];
911 /* Get the position restraint coordinates from the molblock */
912 a_molb = mol*numAtomsInMolecule + a_mol;
913 GMX_ASSERT(a_molb < ssize(molb->posres_xA), "We need a sufficient number of position restraint coordinates");
914 ip->posres.pos0A[XX] = molb->posres_xA[a_molb][XX];
915 ip->posres.pos0A[YY] = molb->posres_xA[a_molb][YY];
916 ip->posres.pos0A[ZZ] = molb->posres_xA[a_molb][ZZ];
917 if (!molb->posres_xB.empty())
919 ip->posres.pos0B[XX] = molb->posres_xB[a_molb][XX];
920 ip->posres.pos0B[YY] = molb->posres_xB[a_molb][YY];
921 ip->posres.pos0B[ZZ] = molb->posres_xB[a_molb][ZZ];
925 ip->posres.pos0B[XX] = ip->posres.pos0A[XX];
926 ip->posres.pos0B[YY] = ip->posres.pos0A[YY];
927 ip->posres.pos0B[ZZ] = ip->posres.pos0A[ZZ];
929 /* Set the parameter index for idef->iparams_posre */
933 /*! \brief Store a flat-bottomed position restraint in idef and iatoms, complex because the parameters are different for each entry */
934 static void add_fbposres(int mol, int a_mol, int numAtomsInMolecule,
935 const gmx_molblock_t *molb,
936 t_iatom *iatoms, const t_iparams *ip_in,
942 /* This flat-bottom position restraint has not been added yet,
943 * so it's index is the current number of position restraints.
945 n = idef->il[F_FBPOSRES].nr/2;
946 if (n+1 > idef->iparams_fbposres_nalloc)
948 idef->iparams_fbposres_nalloc = over_alloc_dd(n+1);
949 srenew(idef->iparams_fbposres, idef->iparams_fbposres_nalloc);
951 ip = &idef->iparams_fbposres[n];
952 /* Copy the force constants */
953 *ip = ip_in[iatoms[0]];
955 /* Get the position restraint coordinats from the molblock */
956 a_molb = mol*numAtomsInMolecule + a_mol;
957 GMX_ASSERT(a_molb < ssize(molb->posres_xA), "We need a sufficient number of position restraint coordinates");
958 /* Take reference positions from A position of normal posres */
959 ip->fbposres.pos0[XX] = molb->posres_xA[a_molb][XX];
960 ip->fbposres.pos0[YY] = molb->posres_xA[a_molb][YY];
961 ip->fbposres.pos0[ZZ] = molb->posres_xA[a_molb][ZZ];
963 /* Note: no B-type for flat-bottom posres */
965 /* Set the parameter index for idef->iparams_posre */
969 /*! \brief Store a virtual site interaction, complex because of PBC and recursion */
970 static void add_vsite(const gmx_ga2la_t &ga2la,
971 gmx::ArrayRef<const int> index,
972 gmx::ArrayRef<const int> rtil,
974 gmx_bool bHomeA, int a, int a_gl, int a_mol,
975 const t_iatom *iatoms,
979 t_iatom tiatoms[1+MAXATOMLIST];
980 int j, ftype_r, nral_r;
982 /* Add this interaction to the local topology */
983 add_ifunc_for_vsites(tiatoms, ga2la, nral, bHomeA, a, a_gl, a_mol, iatoms, &idef->il[ftype]);
987 /* Check for recursion */
988 for (k = 2; k < 1+nral; k++)
990 if ((iatoms[1+nral] & (2<<k)) && (tiatoms[k] < 0))
992 /* This construction atoms is a vsite and not a home atom */
995 fprintf(debug, "Constructing atom %d of vsite atom %d is a vsite and non-home\n", iatoms[k]+1, a_mol+1);
997 /* Find the vsite construction */
999 /* Check all interactions assigned to this atom */
1000 j = index[iatoms[k]];
1001 while (j < index[iatoms[k]+1])
1003 ftype_r = rtil[j++];
1004 nral_r = NRAL(ftype_r);
1005 if (interaction_function[ftype_r].flags & IF_VSITE)
1007 /* Add this vsite (recursion) */
1008 add_vsite(ga2la, index, rtil, ftype_r, nral_r,
1009 FALSE, -1, a_gl+iatoms[k]-iatoms[1], iatoms[k],
1013 j += 1 + nral_rt(ftype_r);
1020 /*! \brief Returns the squared distance between atoms \p i and \p j */
1021 static real dd_dist2(t_pbc *pbc_null, const rvec *x, const int i, int j)
1027 pbc_dx_aiuc(pbc_null, x[i], x[j], dx);
1031 rvec_sub(x[i], x[j], dx);
1037 /*! \brief Append t_blocka block structures 1 to nsrc in src to *dest */
1038 static void combine_blocka(t_blocka *dest,
1039 gmx::ArrayRef<const thread_work_t> src)
1041 int ni = src.back().excl.nr;
1043 for (const thread_work_t &th_work : src)
1045 na += th_work.excl.nra;
1047 if (ni + 1 > dest->nalloc_index)
1049 dest->nalloc_index = over_alloc_large(ni+1);
1050 srenew(dest->index, dest->nalloc_index);
1052 if (dest->nra + na > dest->nalloc_a)
1054 dest->nalloc_a = over_alloc_large(dest->nra+na);
1055 srenew(dest->a, dest->nalloc_a);
1057 for (gmx::index s = 1; s < src.ssize(); s++)
1059 for (int i = dest->nr + 1; i < src[s].excl.nr + 1; i++)
1061 dest->index[i] = dest->nra + src[s].excl.index[i];
1063 for (int i = 0; i < src[s].excl.nra; i++)
1065 dest->a[dest->nra+i] = src[s].excl.a[i];
1067 dest->nr = src[s].excl.nr;
1068 dest->nra += src[s].excl.nra;
1072 /*! \brief Append t_idef structures 1 to nsrc in src to *dest */
1073 static void combine_idef(t_idef *dest,
1074 gmx::ArrayRef<const thread_work_t> src)
1078 for (ftype = 0; ftype < F_NRE; ftype++)
1081 for (gmx::index s = 1; s < src.ssize(); s++)
1083 n += src[s].idef.il[ftype].nr;
1089 ild = &dest->il[ftype];
1091 if (ild->nr + n > ild->nalloc)
1093 ild->nalloc = over_alloc_large(ild->nr+n);
1094 srenew(ild->iatoms, ild->nalloc);
1097 for (gmx::index s = 1; s < src.ssize(); s++)
1099 const t_ilist &ils = src[s].idef.il[ftype];
1101 for (int i = 0; i < ils.nr; i++)
1103 ild->iatoms[ild->nr + i] = ils.iatoms[i];
1109 /* Position restraints need an additional treatment */
1110 if (ftype == F_POSRES || ftype == F_FBPOSRES)
1112 int nposres = dest->il[ftype].nr/2;
1113 // TODO: Simplify this code using std::vector
1114 t_iparams * &iparams_dest = (ftype == F_POSRES ? dest->iparams_posres : dest->iparams_fbposres);
1115 int &posres_nalloc = (ftype == F_POSRES ? dest->iparams_posres_nalloc : dest->iparams_fbposres_nalloc);
1116 if (nposres > posres_nalloc)
1118 posres_nalloc = over_alloc_large(nposres);
1119 srenew(iparams_dest, posres_nalloc);
1122 /* Set nposres to the number of original position restraints in dest */
1123 for (gmx::index s = 1; s < src.ssize(); s++)
1125 nposres -= src[s].idef.il[ftype].nr/2;
1128 for (gmx::index s = 1; s < src.ssize(); s++)
1130 const t_iparams *iparams_src = (ftype == F_POSRES ? src[s].idef.iparams_posres : src[s].idef.iparams_fbposres);
1132 for (int i = 0; i < src[s].idef.il[ftype].nr/2; i++)
1134 /* Correct the index into iparams_posres */
1135 dest->il[ftype].iatoms[nposres*2] = nposres;
1136 /* Copy the position restraint force parameters */
1137 iparams_dest[nposres] = iparams_src[i];
1146 /*! \brief Check and when available assign bonded interactions for local atom i
1149 check_assign_interactions_atom(int i, int i_gl,
1151 int numAtomsInMolecule,
1152 gmx::ArrayRef<const int> index,
1153 gmx::ArrayRef<const int> rtil,
1154 gmx_bool bInterMolInteractions,
1155 int ind_start, int ind_end,
1156 const gmx_domdec_t *dd,
1157 const gmx_domdec_zones_t *zones,
1158 const gmx_molblock_t *molb,
1159 gmx_bool bRCheckMB, const ivec rcheck, gmx_bool bRCheck2B,
1163 const t_iparams *ip_in,
1174 t_iatom tiatoms[1 + MAXATOMLIST];
1176 const int ftype = rtil[j++];
1177 auto iatoms = gmx::constArrayRefFromArray(rtil.data() + j, rtil.size() - j);
1178 const int nral = NRAL(ftype);
1179 if (interaction_function[ftype].flags & IF_VSITE)
1181 assert(!bInterMolInteractions);
1182 /* The vsite construction goes where the vsite itself is */
1185 add_vsite(*dd->ga2la, index, rtil, ftype, nral,
1186 TRUE, i, i_gl, i_mol,
1187 iatoms.data(), idef);
1196 tiatoms[0] = iatoms[0];
1200 assert(!bInterMolInteractions);
1201 /* Assign single-body interactions to the home zone */
1206 if (ftype == F_POSRES)
1208 add_posres(mol, i_mol, numAtomsInMolecule,
1209 molb, tiatoms, ip_in, idef);
1211 else if (ftype == F_FBPOSRES)
1213 add_fbposres(mol, i_mol, numAtomsInMolecule,
1214 molb, tiatoms, ip_in, idef);
1224 /* This is a two-body interaction, we can assign
1225 * analogous to the non-bonded assignments.
1229 if (!bInterMolInteractions)
1231 /* Get the global index using the offset in the molecule */
1232 k_gl = i_gl + iatoms[2] - i_mol;
1238 if (const auto *entry = dd->ga2la->find(k_gl))
1240 int kz = entry->cell;
1245 /* Check zone interaction assignments */
1246 bUse = ((iz < zones->nizone &&
1248 kz >= zones->izone[iz].j0 &&
1249 kz < zones->izone[iz].j1) ||
1250 (kz < zones->nizone &&
1252 iz >= zones->izone[kz].j0 &&
1253 iz < zones->izone[kz].j1));
1256 GMX_ASSERT(ftype != F_CONSTR || (iz == 0 && kz == 0),
1257 "Constraint assigned here should only involve home atoms");
1260 tiatoms[2] = entry->la;
1261 /* If necessary check the cgcm distance */
1263 dd_dist2(pbc_null, cg_cm,
1264 tiatoms[1], tiatoms[2]) >= rc2)
1277 /* Assign this multi-body bonded interaction to
1278 * the local node if we have all the atoms involved
1279 * (local or communicated) and the minimum zone shift
1280 * in each dimension is zero, for dimensions
1281 * with 2 DD cells an extra check may be necessary.
1283 ivec k_zero, k_plus;
1289 for (k = 1; k <= nral && bUse; k++)
1292 if (!bInterMolInteractions)
1294 /* Get the global index using the offset in the molecule */
1295 k_gl = i_gl + iatoms[k] - i_mol;
1301 const auto *entry = dd->ga2la->find(k_gl);
1302 if (entry == nullptr || entry->cell >= zones->n)
1304 /* We do not have this atom of this interaction
1305 * locally, or it comes from more than one cell
1314 tiatoms[k] = entry->la;
1315 for (d = 0; d < DIM; d++)
1317 if (zones->shift[entry->cell][d] == 0)
1329 (k_zero[XX] != 0) && (k_zero[YY] != 0) && (k_zero[ZZ] != 0));
1334 for (d = 0; (d < DIM && bUse); d++)
1336 /* Check if the cg_cm distance falls within
1337 * the cut-off to avoid possible multiple
1338 * assignments of bonded interactions.
1342 dd_dist2(pbc_null, cg_cm,
1343 tiatoms[k_zero[d]], tiatoms[k_plus[d]]) >= rc2)
1352 /* Add this interaction to the local topology */
1353 add_ifunc(nral, tiatoms, &idef->il[ftype]);
1354 /* Sum so we can check in global_stat
1355 * if we have everything.
1358 !(interaction_function[ftype].flags & IF_LIMZERO))
1368 /*! \brief This function looks up and assigns bonded interactions for zone iz.
1370 * With thread parallelizing each thread acts on a different atom range:
1371 * at_start to at_end.
1373 static int make_bondeds_zone(gmx_domdec_t *dd,
1374 const gmx_domdec_zones_t *zones,
1375 const std::vector<gmx_molblock_t> &molb,
1376 gmx_bool bRCheckMB, ivec rcheck, gmx_bool bRCheck2B,
1378 t_pbc *pbc_null, rvec *cg_cm,
1379 const t_iparams *ip_in,
1382 gmx::RangePartitioning::Block atomRange)
1384 int mb, mt, mol, i_mol;
1386 gmx_reverse_top_t *rt;
1389 rt = dd->reverse_top;
1391 bBCheck = rt->bBCheck;
1395 for (int i : atomRange)
1397 /* Get the global atom number */
1398 const int i_gl = dd->globalAtomIndices[i];
1399 global_atomnr_to_moltype_ind(rt, i_gl, &mb, &mt, &mol, &i_mol);
1400 /* Check all intramolecular interactions assigned to this atom */
1401 gmx::ArrayRef<const int> index = rt->ril_mt[mt].index;
1402 gmx::ArrayRef<const t_iatom> rtil = rt->ril_mt[mt].il;
1404 check_assign_interactions_atom(i, i_gl, mol, i_mol,
1405 rt->ril_mt[mt].numAtomsInMolecule,
1407 index[i_mol], index[i_mol+1],
1410 bRCheckMB, rcheck, bRCheck2B, rc2,
1420 if (rt->bIntermolecularInteractions)
1422 /* Check all intermolecular interactions assigned to this atom */
1423 index = rt->ril_intermol.index;
1424 rtil = rt->ril_intermol.il;
1426 check_assign_interactions_atom(i, i_gl, mol, i_mol,
1427 rt->ril_mt[mt].numAtomsInMolecule,
1429 index[i_gl], index[i_gl + 1],
1432 bRCheckMB, rcheck, bRCheck2B, rc2,
1443 return nbonded_local;
1446 /*! \brief Set the exclusion data for i-zone \p iz for the case of no exclusions */
1447 static void set_no_exclusions_zone(const gmx_domdec_zones_t *zones,
1451 for (int a = zones->cg_range[iz]; a < zones->cg_range[iz + 1]; a++)
1453 lexcls->index[a + 1] = lexcls->nra;
1457 /*! \brief Set the exclusion data for i-zone \p iz
1459 * This is a legacy version for the group scheme of the same routine below.
1460 * Here charge groups and distance checks to ensure unique exclusions
1463 static int make_exclusions_zone_cg(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
1464 const std::vector<gmx_moltype_t> &moltype,
1465 gmx_bool bRCheck, real rc2,
1466 t_pbc *pbc_null, rvec *cg_cm,
1470 int cg_start, int cg_end)
1474 const t_blocka *excls;
1476 const gmx_ga2la_t &ga2la = *dd->ga2la;
1478 // TODO: Replace this by a more standard range
1479 const gmx::RangePartitioning::Block jRange(zones->izone[iz].jcg0,
1480 zones->izone[iz].jcg1);
1482 n_excl_at_max = dd->reverse_top->n_excl_at_max;
1484 /* We set the end index, but note that we might not start at zero here */
1485 lexcls->nr = cg_end;
1487 int n = lexcls->nra;
1489 for (int la = cg_start; la < cg_end; la++)
1491 if (n + (cg_end - cg_start)*n_excl_at_max > lexcls->nalloc_a)
1493 lexcls->nalloc_a = over_alloc_large(n + (cg_end - cg_start)*n_excl_at_max);
1494 srenew(lexcls->a, lexcls->nalloc_a);
1496 if (GET_CGINFO_EXCL_INTER(cginfo[la]) ||
1497 !GET_CGINFO_EXCL_INTRA(cginfo[la]))
1499 /* Copy the exclusions from the global top */
1500 lexcls->index[la] = n;
1501 int a_gl = dd->globalAtomIndices[la];
1503 global_atomnr_to_moltype_ind(dd->reverse_top, a_gl, &mb, &mt, &mol, &a_mol);
1504 excls = &moltype[mt].excls;
1505 for (int j = excls->index[a_mol]; j < excls->index[a_mol+1]; j++)
1507 int aj_mol = excls->a[j];
1508 /* Since exclusions are pair interactions,
1509 * just like non-bonded interactions,
1510 * they can be assigned properly up
1511 * to the DD cutoff (not cutoff_min as
1512 * for the other bonded interactions).
1514 if (const auto *jEntry = ga2la.find(a_gl + aj_mol - a_mol))
1516 if (iz == 0 && jEntry->cell == 0)
1518 lexcls->a[n++] = jEntry->la;
1519 /* Check to avoid double counts */
1520 if (jEntry->la > la)
1525 else if (jRange.inRange(jEntry->la) &&
1527 dd_dist2(pbc_null, cg_cm, la, jEntry->la) < rc2))
1529 /* jla > la, since jRange.begin() > la */
1530 lexcls->a[n++] = jEntry->la;
1538 /* There are no inter-atomic excls and this atom is self-excluded.
1539 * These exclusions are only required for zone 0,
1540 * since other zones do not see themselves.
1544 lexcls->index[la] = n;
1545 lexcls->a[n++] = la;
1549 lexcls->index[la] = n;
1554 lexcls->index[lexcls->nr] = n;
1560 /*! \brief Set the exclusion data for i-zone \p iz */
1561 static void make_exclusions_zone(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
1562 const std::vector<gmx_moltype_t> &moltype,
1563 const int *cginfo, t_blocka *lexcls, int iz,
1564 int at_start, int at_end,
1565 const gmx::ArrayRef<const int> intermolecularExclusionGroup)
1567 int n_excl_at_max, n, at;
1569 const gmx_ga2la_t &ga2la = *dd->ga2la;
1571 // TODO: Replace this by a more standard range
1572 const gmx::RangePartitioning::Block jRange(zones->izone[iz].jcg0,
1573 zones->izone[iz].jcg1);
1575 n_excl_at_max = dd->reverse_top->n_excl_at_max;
1577 /* We set the end index, but note that we might not start at zero here */
1578 lexcls->nr = at_end;
1581 for (at = at_start; at < at_end; at++)
1583 if (n + 1000 > lexcls->nalloc_a)
1585 lexcls->nalloc_a = over_alloc_large(n + 1000);
1586 srenew(lexcls->a, lexcls->nalloc_a);
1589 if (GET_CGINFO_EXCL_INTER(cginfo[at]))
1591 int a_gl, mb, mt, mol, a_mol, j;
1592 const t_blocka *excls;
1594 if (n + n_excl_at_max > lexcls->nalloc_a)
1596 lexcls->nalloc_a = over_alloc_large(n + n_excl_at_max);
1597 srenew(lexcls->a, lexcls->nalloc_a);
1600 /* Copy the exclusions from the global top */
1601 lexcls->index[at] = n;
1602 a_gl = dd->globalAtomIndices[at];
1603 global_atomnr_to_moltype_ind(dd->reverse_top, a_gl,
1604 &mb, &mt, &mol, &a_mol);
1605 excls = &moltype[mt].excls;
1606 for (j = excls->index[a_mol]; j < excls->index[a_mol + 1]; j++)
1608 const int aj_mol = excls->a[j];
1610 if (const auto *jEntry = ga2la.find(a_gl + aj_mol - a_mol))
1612 /* This check is not necessary, but it can reduce
1613 * the number of exclusions in the list, which in turn
1614 * can speed up the pair list construction a bit.
1616 if (jRange.inRange(jEntry->la))
1618 lexcls->a[n++] = jEntry->la;
1625 /* We don't need exclusions for this atom */
1626 lexcls->index[at] = n;
1629 bool isExcludedAtom = !intermolecularExclusionGroup.empty() &&
1630 std::find(intermolecularExclusionGroup.begin(),
1631 intermolecularExclusionGroup.end(),
1632 dd->globalAtomIndices[at]) !=
1633 intermolecularExclusionGroup.end();
1637 if (n + intermolecularExclusionGroup.ssize() > lexcls->nalloc_a)
1640 over_alloc_large(n + intermolecularExclusionGroup.size());
1641 srenew(lexcls->a, lexcls->nalloc_a);
1643 for (int qmAtomGlobalIndex : intermolecularExclusionGroup)
1645 if (const auto *entry = dd->ga2la->find(qmAtomGlobalIndex))
1647 lexcls->a[n++] = entry->la;
1653 lexcls->index[lexcls->nr] = n;
1658 /*! \brief Ensure we have enough space in \p ba for \p nindex_max indices */
1659 static void check_alloc_index(t_blocka *ba, int nindex_max)
1661 if (nindex_max+1 > ba->nalloc_index)
1663 ba->nalloc_index = over_alloc_dd(nindex_max+1);
1664 srenew(ba->index, ba->nalloc_index);
1668 /*! \brief Ensure that we have enough space for exclusion storate in \p lexcls */
1669 static void check_exclusions_alloc(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
1672 const int nr = zones->izone[zones->nizone - 1].cg1;
1674 check_alloc_index(lexcls, nr);
1676 for (size_t thread = 1; thread < dd->reverse_top->th_work.size(); thread++)
1678 check_alloc_index(&dd->reverse_top->th_work[thread].excl, nr);
1682 /*! \brief Set the total count indexes for the local exclusions, needed by several functions */
1683 static void finish_local_exclusions(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
1686 // TODO: Replace this by a more standard range
1687 const gmx::RangePartitioning::Block nonhomeIzonesAtomRange(zones->izone[0].cg1,
1688 zones->izone[zones->nizone - 1].cg1);
1690 if (dd->n_intercg_excl == 0)
1692 /* There are no exclusions involving non-home charge groups,
1693 * but we need to set the indices for neighborsearching.
1695 for (int la : nonhomeIzonesAtomRange)
1697 lexcls->index[la] = lexcls->nra;
1700 /* nr is only used to loop over the exclusions for Ewald and RF,
1701 * so we can set it to the number of home atoms for efficiency.
1703 lexcls->nr = nonhomeIzonesAtomRange.begin();
1707 lexcls->nr = nonhomeIzonesAtomRange.end();
1711 /*! \brief Clear a t_idef struct */
1712 static void clear_idef(t_idef *idef)
1716 /* Clear the counts */
1717 for (ftype = 0; ftype < F_NRE; ftype++)
1719 idef->il[ftype].nr = 0;
1723 /*! \brief Generate and store all required local bonded interactions in \p idef and local exclusions in \p lexcls */
1724 static int make_local_bondeds_excls(gmx_domdec_t *dd,
1725 gmx_domdec_zones_t *zones,
1726 const gmx_mtop_t *mtop,
1728 gmx_bool bRCheckMB, ivec rcheck, gmx_bool bRCheck2B,
1730 t_pbc *pbc_null, rvec *cg_cm,
1732 t_blocka *lexcls, int *excl_count)
1734 int nzone_bondeds, nzone_excl;
1735 int izone, cg0, cg1;
1739 gmx_reverse_top_t *rt;
1741 if (dd->reverse_top->bInterCGInteractions)
1743 nzone_bondeds = zones->n;
1747 /* Only single charge group (or atom) molecules, so interactions don't
1748 * cross zone boundaries and we only need to assign in the home zone.
1753 if (dd->n_intercg_excl > 0)
1755 /* We only use exclusions from i-zones to i- and j-zones */
1756 nzone_excl = zones->nizone;
1760 /* There are no inter-cg exclusions and only zone 0 sees itself */
1764 check_exclusions_alloc(dd, zones, lexcls);
1766 rt = dd->reverse_top;
1770 /* Clear the counts */
1778 for (izone = 0; izone < nzone_bondeds; izone++)
1780 cg0 = zones->cg_range[izone];
1781 cg1 = zones->cg_range[izone + 1];
1783 const int numThreads = rt->th_work.size();
1784 #pragma omp parallel for num_threads(numThreads) schedule(static)
1785 for (thread = 0; thread < numThreads; thread++)
1793 cg0t = cg0 + ((cg1 - cg0)* thread )/numThreads;
1794 cg1t = cg0 + ((cg1 - cg0)*(thread+1))/numThreads;
1802 idef_t = &rt->th_work[thread].idef;
1806 rt->th_work[thread].nbonded =
1807 make_bondeds_zone(dd, zones,
1809 bRCheckMB, rcheck, bRCheck2B, rc2,
1810 pbc_null, cg_cm, idef->iparams,
1813 gmx::RangePartitioning::Block(cg0t, cg1t));
1815 if (izone < nzone_excl)
1823 excl_t = &rt->th_work[thread].excl;
1828 if (!rt->bExclRequired)
1830 /* No charge groups and no distance check required */
1831 make_exclusions_zone(dd, zones, mtop->moltype, cginfo,
1832 excl_t, izone, cg0t,
1834 mtop->intermolecularExclusionGroup);
1838 rt->th_work[thread].excl_count =
1839 make_exclusions_zone_cg(dd, zones,
1840 mtop->moltype, bRCheck2B, rc2,
1841 pbc_null, cg_cm, cginfo,
1848 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
1851 if (rt->th_work.size() > 1)
1853 combine_idef(idef, rt->th_work);
1856 for (const thread_work_t &th_work : rt->th_work)
1858 nbonded_local += th_work.nbonded;
1861 if (izone < nzone_excl)
1863 if (rt->th_work.size() > 1)
1865 combine_blocka(lexcls, rt->th_work);
1868 for (const thread_work_t &th_work : rt->th_work)
1870 *excl_count += th_work.excl_count;
1875 /* Some zones might not have exclusions, but some code still needs to
1876 * loop over the index, so we set the indices here.
1878 for (izone = nzone_excl; izone < zones->nizone; izone++)
1880 set_no_exclusions_zone(zones, izone, lexcls);
1883 finish_local_exclusions(dd, zones, lexcls);
1886 fprintf(debug, "We have %d exclusions, check count %d\n",
1887 lexcls->nra, *excl_count);
1890 return nbonded_local;
1893 void dd_make_local_top(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
1894 int npbcdim, matrix box,
1895 rvec cellsize_min, const ivec npulse,
1898 const gmx_mtop_t &mtop, gmx_localtop_t *ltop)
1900 gmx_bool bRCheckMB, bRCheck2B;
1904 t_pbc pbc, *pbc_null = nullptr;
1908 fprintf(debug, "Making local topology\n");
1914 if (dd->reverse_top->bInterCGInteractions)
1916 /* We need to check to which cell bondeds should be assigned */
1917 rc = dd_cutoff_twobody(dd);
1920 fprintf(debug, "Two-body bonded cut-off distance is %g\n", rc);
1923 /* Should we check cg_cm distances when assigning bonded interactions? */
1924 for (d = 0; d < DIM; d++)
1927 /* Only need to check for dimensions where the part of the box
1928 * that is not communicated is smaller than the cut-off.
1930 if (d < npbcdim && dd->nc[d] > 1 &&
1931 (dd->nc[d] - npulse[d])*cellsize_min[d] < 2*rc)
1938 /* Check for interactions between two atoms,
1939 * where we can allow interactions up to the cut-off,
1940 * instead of up to the smallest cell dimension.
1947 "dim %d cellmin %f bonded rcheck[%d] = %d, bRCheck2B = %s\n",
1948 d, cellsize_min[d], d, rcheck[d], gmx::boolToString(bRCheck2B));
1951 if (bRCheckMB || bRCheck2B)
1955 pbc_null = set_pbc_dd(&pbc, fr->ePBC, dd->nc, TRUE, box);
1965 make_local_bondeds_excls(dd, zones, &mtop, fr->cginfo.data(),
1966 bRCheckMB, rcheck, bRCheck2B, rc,
1967 pbc_null, cgcm_or_x,
1969 <op->excls, &nexcl);
1971 /* The ilist is not sorted yet,
1972 * we can only do this when we have the charge arrays.
1974 ltop->idef.ilsort = ilsortUNKNOWN;
1976 if (dd->reverse_top->bExclRequired)
1978 dd->nbonded_local += nexcl;
1981 ltop->atomtypes = mtop.atomtypes;
1984 void dd_sort_local_top(gmx_domdec_t *dd, const t_mdatoms *mdatoms,
1985 gmx_localtop_t *ltop)
1987 if (dd->reverse_top->ilsort == ilsortNO_FE)
1989 ltop->idef.ilsort = ilsortNO_FE;
1993 gmx_sort_ilist_fe(<op->idef, mdatoms->chargeA, mdatoms->chargeB);
1997 void dd_init_local_top(const gmx_mtop_t &top_global,
1998 gmx_localtop_t *top)
2000 /* TODO: Get rid of the const casts below, e.g. by using a reference */
2001 top->idef.ntypes = top_global.ffparams.numTypes();
2002 top->idef.atnr = top_global.ffparams.atnr;
2003 top->idef.functype = const_cast<t_functype *>(top_global.ffparams.functype.data());
2004 top->idef.iparams = const_cast<t_iparams *>(top_global.ffparams.iparams.data());
2005 top->idef.fudgeQQ = top_global.ffparams.fudgeQQ;
2006 top->idef.cmap_grid = new gmx_cmap_t;
2007 *top->idef.cmap_grid = top_global.ffparams.cmap_grid;
2009 top->idef.ilsort = ilsortUNKNOWN;
2010 top->useInDomainDecomp_ = true;
2013 void dd_init_local_state(gmx_domdec_t *dd,
2014 const t_state *state_global, t_state *state_local)
2016 int buf[NITEM_DD_INIT_LOCAL_STATE];
2020 buf[0] = state_global->flags;
2021 buf[1] = state_global->ngtc;
2022 buf[2] = state_global->nnhpres;
2023 buf[3] = state_global->nhchainlength;
2024 buf[4] = state_global->dfhist ? state_global->dfhist->nlambda : 0;
2026 dd_bcast(dd, NITEM_DD_INIT_LOCAL_STATE*sizeof(int), buf);
2028 init_gtc_state(state_local, buf[1], buf[2], buf[3]);
2029 init_dfhist_state(state_local, buf[4]);
2030 state_local->flags = buf[0];
2033 /*! \brief Check if a link is stored in \p link between charge groups \p cg_gl and \p cg_gl_j and if not so, store a link */
2034 static void check_link(t_blocka *link, int cg_gl, int cg_gl_j)
2040 for (k = link->index[cg_gl]; k < link->index[cg_gl+1]; k++)
2042 GMX_RELEASE_ASSERT(link->a, "Inconsistent NULL pointer while making charge-group links");
2043 if (link->a[k] == cg_gl_j)
2050 GMX_RELEASE_ASSERT(link->a || link->index[cg_gl+1]+1 > link->nalloc_a,
2051 "Inconsistent allocation of link");
2052 /* Add this charge group link */
2053 if (link->index[cg_gl+1]+1 > link->nalloc_a)
2055 link->nalloc_a = over_alloc_large(link->index[cg_gl+1]+1);
2056 srenew(link->a, link->nalloc_a);
2058 link->a[link->index[cg_gl+1]] = cg_gl_j;
2059 link->index[cg_gl+1]++;
2063 /*! \brief Return a vector of the charge group index for all atoms */
2064 static std::vector<int> make_at2cg(const t_block &cgs)
2066 std::vector<int> at2cg(cgs.index[cgs.nr]);
2067 for (int cg = 0; cg < cgs.nr; cg++)
2069 for (int a = cgs.index[cg]; a < cgs.index[cg + 1]; a++)
2078 t_blocka *make_charge_group_links(const gmx_mtop_t *mtop, gmx_domdec_t *dd,
2079 cginfo_mb_t *cginfo_mb)
2081 gmx_bool bExclRequired;
2083 cginfo_mb_t *cgi_mb;
2085 /* For each charge group make a list of other charge groups
2086 * in the system that a linked to it via bonded interactions
2087 * which are also stored in reverse_top.
2090 bExclRequired = dd->reverse_top->bExclRequired;
2092 reverse_ilist_t ril_intermol;
2093 if (mtop->bIntermolecularInteractions)
2095 if (ncg_mtop(mtop) < mtop->natoms)
2097 gmx_fatal(FARGS, "The combination of intermolecular interactions, charge groups and domain decomposition is not supported. Use cutoff-scheme=Verlet (which removes the charge groups) or run without domain decomposition.");
2102 atoms.nr = mtop->natoms;
2103 atoms.atom = nullptr;
2105 GMX_RELEASE_ASSERT(mtop->intermolecular_ilist, "We should have an ilist when intermolecular interactions are on");
2107 make_reverse_ilist(*mtop->intermolecular_ilist,
2109 FALSE, FALSE, FALSE, TRUE, &ril_intermol);
2113 snew(link->index, ncg_mtop(mtop)+1);
2120 for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
2122 const gmx_molblock_t &molb = mtop->molblock[mb];
2127 const gmx_moltype_t &molt = mtop->moltype[molb.type];
2128 const t_block &cgs = molt.cgs;
2129 const t_blocka &excls = molt.excls;
2130 std::vector<int> a2c = make_at2cg(cgs);
2131 /* Make a reverse ilist in which the interactions are linked
2132 * to all atoms, not only the first atom as in gmx_reverse_top.
2133 * The constraints are discarded here.
2135 reverse_ilist_t ril;
2136 make_reverse_ilist(molt.ilist, &molt.atoms,
2137 FALSE, FALSE, FALSE, TRUE, &ril);
2139 cgi_mb = &cginfo_mb[mb];
2142 for (mol = 0; mol < (mtop->bIntermolecularInteractions ? molb.nmol : 1); mol++)
2144 for (int cg = 0; cg < cgs.nr; cg++)
2146 int cg_gl = cg_offset + cg;
2147 link->index[cg_gl+1] = link->index[cg_gl];
2148 for (int a = cgs.index[cg]; a < cgs.index[cg + 1]; a++)
2150 int i = ril.index[a];
2151 while (i < ril.index[a+1])
2153 int ftype = ril.il[i++];
2154 int nral = NRAL(ftype);
2155 /* Skip the ifunc index */
2157 for (int j = 0; j < nral; j++)
2159 int aj = ril.il[i + j];
2162 check_link(link, cg_gl, cg_offset+a2c[aj]);
2165 i += nral_rt(ftype);
2169 /* Exclusions always go both ways */
2170 for (int j = excls.index[a]; j < excls.index[a + 1]; j++)
2172 int aj = excls.a[j];
2175 check_link(link, cg_gl, cg_offset+a2c[aj]);
2180 if (mtop->bIntermolecularInteractions)
2182 int i = ril_intermol.index[a];
2183 while (i < ril_intermol.index[a+1])
2185 int ftype = ril_intermol.il[i++];
2186 int nral = NRAL(ftype);
2187 /* Skip the ifunc index */
2189 for (int j = 0; j < nral; j++)
2191 /* Here we assume we have no charge groups;
2192 * this has been checked above.
2194 int aj = ril_intermol.il[i + j];
2195 check_link(link, cg_gl, aj);
2197 i += nral_rt(ftype);
2201 if (link->index[cg_gl+1] - link->index[cg_gl] > 0)
2203 SET_CGINFO_BOND_INTER(cgi_mb->cginfo[cg]);
2208 cg_offset += cgs.nr;
2210 int nlink_mol = link->index[cg_offset] - link->index[cg_offset - cgs.nr];
2214 fprintf(debug, "molecule type '%s' %d cgs has %d cg links through bonded interac.\n", *molt.name, cgs.nr, nlink_mol);
2217 if (molb.nmol > mol)
2219 /* Copy the data for the rest of the molecules in this block */
2220 link->nalloc_a += (molb.nmol - mol)*nlink_mol;
2221 srenew(link->a, link->nalloc_a);
2222 for (; mol < molb.nmol; mol++)
2224 for (int cg = 0; cg < cgs.nr; cg++)
2226 int cg_gl = cg_offset + cg;
2227 link->index[cg_gl + 1] =
2228 link->index[cg_gl + 1 - cgs.nr] + nlink_mol;
2229 for (int j = link->index[cg_gl]; j < link->index[cg_gl+1]; j++)
2231 link->a[j] = link->a[j - nlink_mol] + cgs.nr;
2233 if (link->index[cg_gl+1] - link->index[cg_gl] > 0 &&
2234 cg_gl - cgi_mb->cg_start < cgi_mb->cg_mod)
2236 SET_CGINFO_BOND_INTER(cgi_mb->cginfo[cg_gl - cgi_mb->cg_start]);
2240 cg_offset += cgs.nr;
2247 fprintf(debug, "Of the %d charge groups %d are linked via bonded interactions\n", ncg_mtop(mtop), ncgi);
2258 } bonded_distance_t;
2260 /*! \brief Compare distance^2 \p r2 against the distance in \p bd and if larger store it along with \p ftype and atom indices \p a1 and \p a2 */
2261 static void update_max_bonded_distance(real r2, int ftype, int a1, int a2,
2262 bonded_distance_t *bd)
2273 /*! \brief Set the distance, function type and atom indices for the longest distance between charge-groups of molecule type \p molt for two-body and multi-body bonded interactions */
2274 static void bonded_cg_distance_mol(const gmx_moltype_t *molt,
2275 const std::vector<int> &at2cg,
2276 gmx_bool bBCheck, gmx_bool bExcl, rvec *cg_cm,
2277 bonded_distance_t *bd_2b,
2278 bonded_distance_t *bd_mb)
2280 for (int ftype = 0; ftype < F_NRE; ftype++)
2282 if (dd_check_ftype(ftype, bBCheck, FALSE, FALSE))
2284 const auto &il = molt->ilist[ftype];
2285 int nral = NRAL(ftype);
2288 for (int i = 0; i < il.size(); i += 1+nral)
2290 for (int ai = 0; ai < nral; ai++)
2292 int cgi = at2cg[il.iatoms[i+1+ai]];
2293 for (int aj = ai + 1; aj < nral; aj++)
2295 int cgj = at2cg[il.iatoms[i+1+aj]];
2298 real rij2 = distance2(cg_cm[cgi], cg_cm[cgj]);
2300 update_max_bonded_distance(rij2, ftype,
2303 (nral == 2) ? bd_2b : bd_mb);
2313 const t_blocka *excls = &molt->excls;
2314 for (int ai = 0; ai < excls->nr; ai++)
2316 int cgi = at2cg[ai];
2317 for (int j = excls->index[ai]; j < excls->index[ai+1]; j++)
2319 int cgj = at2cg[excls->a[j]];
2322 real rij2 = distance2(cg_cm[cgi], cg_cm[cgj]);
2324 /* There is no function type for exclusions, use -1 */
2325 update_max_bonded_distance(rij2, -1, ai, excls->a[j], bd_2b);
2332 /*! \brief Set the distance, function type and atom indices for the longest atom distance involved in intermolecular interactions for two-body and multi-body bonded interactions */
2333 static void bonded_distance_intermol(const InteractionLists &ilists_intermol,
2335 const rvec *x, int ePBC, const matrix box,
2336 bonded_distance_t *bd_2b,
2337 bonded_distance_t *bd_mb)
2341 set_pbc(&pbc, ePBC, box);
2343 for (int ftype = 0; ftype < F_NRE; ftype++)
2345 if (dd_check_ftype(ftype, bBCheck, FALSE, FALSE))
2347 const auto &il = ilists_intermol[ftype];
2348 int nral = NRAL(ftype);
2350 /* No nral>1 check here, since intermol interactions always
2351 * have nral>=2 (and the code is also correct for nral=1).
2353 for (int i = 0; i < il.size(); i += 1+nral)
2355 for (int ai = 0; ai < nral; ai++)
2357 int atom_i = il.iatoms[i + 1 + ai];
2359 for (int aj = ai + 1; aj < nral; aj++)
2364 int atom_j = il.iatoms[i + 1 + aj];
2366 pbc_dx(&pbc, x[atom_i], x[atom_j], dx);
2370 update_max_bonded_distance(rij2, ftype,
2372 (nral == 2) ? bd_2b : bd_mb);
2380 //! Returns whether \p molt has at least one virtual site
2381 static bool moltypeHasVsite(const gmx_moltype_t &molt)
2383 bool hasVsite = false;
2384 for (int i = 0; i < F_NRE; i++)
2386 if ((interaction_function[i].flags & IF_VSITE) &&
2387 molt.ilist[i].size() > 0)
2396 //! Compute charge group centers of mass for molecule \p molt
2397 static void get_cgcm_mol(const gmx_moltype_t *molt,
2398 const gmx_ffparams_t *ffparams,
2399 int ePBC, t_graph *graph, const matrix box,
2400 const rvec *x, rvec *xs, rvec *cg_cm)
2404 if (ePBC != epbcNONE)
2406 mk_mshift(nullptr, graph, ePBC, box, x);
2408 shift_x(graph, box, x, xs);
2409 /* By doing an extra mk_mshift the molecules that are broken
2410 * because they were e.g. imported from another software
2411 * will be made whole again. Such are the healing powers
2414 mk_mshift(nullptr, graph, ePBC, box, xs);
2418 /* We copy the coordinates so the original coordinates remain
2419 * unchanged, just to be 100% sure that we do not affect
2420 * binary reproducibility of simulations.
2422 n = molt->cgs.index[molt->cgs.nr];
2423 for (i = 0; i < n; i++)
2425 copy_rvec(x[i], xs[i]);
2429 if (moltypeHasVsite(*molt))
2431 /* Convert to old, deprecated format */
2432 t_ilist ilist[F_NRE];
2433 for (int ftype = 0; ftype < F_NRE; ftype++)
2435 if (interaction_function[ftype].flags & IF_VSITE)
2437 ilist[ftype].nr = molt->ilist[ftype].size();
2438 ilist[ftype].iatoms = const_cast<int *>(molt->ilist[ftype].iatoms.data());
2442 construct_vsites(nullptr, xs, 0.0, nullptr,
2443 ffparams->iparams.data(), ilist,
2444 epbcNONE, TRUE, nullptr, nullptr);
2447 calc_cgcm(nullptr, 0, molt->cgs.nr, &molt->cgs, xs, cg_cm);
2450 void dd_bonded_cg_distance(const gmx::MDLogger &mdlog,
2451 const gmx_mtop_t *mtop,
2452 const t_inputrec *ir,
2453 const rvec *x, const matrix box,
2455 real *r_2b, real *r_mb)
2457 gmx_bool bExclRequired;
2461 bonded_distance_t bd_2b = { 0, -1, -1, -1 };
2462 bonded_distance_t bd_mb = { 0, -1, -1, -1 };
2464 bExclRequired = inputrecExclForces(ir);
2469 for (const gmx_molblock_t &molb : mtop->molblock)
2471 const gmx_moltype_t &molt = mtop->moltype[molb.type];
2472 if (molt.cgs.nr == 1 || molb.nmol == 0)
2474 at_offset += molb.nmol*molt.atoms.nr;
2478 if (ir->ePBC != epbcNONE)
2480 mk_graph_moltype(molt, &graph);
2483 std::vector<int> at2cg = make_at2cg(molt.cgs);
2484 snew(xs, molt.atoms.nr);
2485 snew(cg_cm, molt.cgs.nr);
2486 for (int mol = 0; mol < molb.nmol; mol++)
2488 get_cgcm_mol(&molt, &mtop->ffparams, ir->ePBC, &graph, box,
2489 x+at_offset, xs, cg_cm);
2491 bonded_distance_t bd_mol_2b = { 0, -1, -1, -1 };
2492 bonded_distance_t bd_mol_mb = { 0, -1, -1, -1 };
2494 bonded_cg_distance_mol(&molt, at2cg, bBCheck, bExclRequired, cg_cm,
2495 &bd_mol_2b, &bd_mol_mb);
2497 /* Process the mol data adding the atom index offset */
2498 update_max_bonded_distance(bd_mol_2b.r2, bd_mol_2b.ftype,
2499 at_offset + bd_mol_2b.a1,
2500 at_offset + bd_mol_2b.a2,
2502 update_max_bonded_distance(bd_mol_mb.r2, bd_mol_mb.ftype,
2503 at_offset + bd_mol_mb.a1,
2504 at_offset + bd_mol_mb.a2,
2507 at_offset += molt.atoms.nr;
2511 if (ir->ePBC != epbcNONE)
2518 if (mtop->bIntermolecularInteractions)
2520 if (ncg_mtop(mtop) < mtop->natoms)
2522 gmx_fatal(FARGS, "The combination of intermolecular interactions, charge groups and domain decomposition is not supported. Use cutoff-scheme=Verlet (which removes the charge groups) or run without domain decomposition.");
2525 GMX_RELEASE_ASSERT(mtop->intermolecular_ilist, "We should have an ilist when intermolecular interactions are on");
2527 bonded_distance_intermol(*mtop->intermolecular_ilist,
2533 *r_2b = sqrt(bd_2b.r2);
2534 *r_mb = sqrt(bd_mb.r2);
2536 if (*r_2b > 0 || *r_mb > 0)
2538 GMX_LOG(mdlog.info).appendText("Initial maximum distances in bonded interactions:");
2541 GMX_LOG(mdlog.info).appendTextFormatted(
2542 " two-body bonded interactions: %5.3f nm, %s, atoms %d %d",
2543 *r_2b, (bd_2b.ftype >= 0) ? interaction_function[bd_2b.ftype].longname : "Exclusion",
2544 bd_2b.a1 + 1, bd_2b.a2 + 1);
2548 GMX_LOG(mdlog.info).appendTextFormatted(
2549 " multi-body bonded interactions: %5.3f nm, %s, atoms %d %d",
2550 *r_mb, interaction_function[bd_mb.ftype].longname,
2551 bd_mb.a1 + 1, bd_mb.a2 + 1);